Genetic diversity of second generation-parental germplasm of masson pine revealed by SSR markers and establishment of a core germplasm collection

2021 ◽  
pp. 1-8
Author(s):  
Hanbo Yang ◽  
Qinghua Liu ◽  
Rui Zhang ◽  
Zhichun Zhou
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Second Generation ◽  
Germplasm Collection ◽  
Masson Pine ◽  
Core Germplasm

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)

2016 ◽  
Vol 7 (2) ◽  
pp. 76
Author(s):  
Dwinita Wikan Utami ◽  
Sutoro Sutoro ◽  
Nurul Hidayatun ◽  
Andari Risliawati ◽  
Ida Hanarida
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Heading Date ◽  
Germplasm Collection ◽  
Dna Fingerprint ◽  
Early Maturity ◽  
Plant Variety ◽  
Variety Protection ◽  
Genetic Analyzer

<p>Genetic Diversity of 96 Accession of Rice Germplasm<br />Using 30 SSR Markers Linked to Heading Date Genes (HD<br />Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun,<br />Andari Risliawati, and Ida Hanarida. Rice with early<br />maturity is one of an important genetic resources in rice<br />germplasm collection. Characterization and identification of<br />genetic diversity is an important issue for plant variety protection.<br />Molecular identification by microsatellite markers<br />using Genetic Analyzer enables resolve of this issue. The<br />objective of this research is to identify the genetic diversity of<br />96 rice accessions based on their specific DNA fingerprint<br />using microsatellite markers. A total of 96 accessions consisting<br />of a diverse variety of maturity classification were<br />genotyped with 30 SSR markers linked to HD genes which<br />spread out in 12 chromosomes of rice geneome. The total<br />297 alleles were detected indicated the level of marker<br />informativeness. RM5607 generated 7 allele with the size<br />range from 103 to 197 and the highest PIC at 0.90. RM3571<br />(linked to HD12 gene) has a significant value associated with<br />varieties which have early maturity trait. Clustering analysis<br />showed the cluster based on Sub Species genome background<br />and on early maturity trait.</p>

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 108-114 ◽  
Author(s):  
José Miguel Soriano ◽  
Carlos Romero ◽  
Santiago Vilanova ◽  
Gerardo Llácer ◽  
María Luisa Badenes
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Malus Domestica ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Mean Value ◽  
Eriobotrya Japonica ◽  
Fixation Index ◽  
Group Method ◽  
Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

scholarly journals Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers

Genome ◽  
2017 ◽  
Vol 60 (3) ◽  
pp. 193-200 ◽  
Author(s):  
M.L. Wang ◽  
M. Dzievit ◽  
Z. Chen ◽  
J.B. Morris ◽  
J.E. Norris ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Ssr Markers ◽  
Oil Content ◽  
Germplasm Collection ◽  
Germplasm Management ◽  
The Us

Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.

scholarly journals Erratum to: Development of SSR markers and assessment of genetic diversity of adzuki bean in the Chinese germplasm collection

2017 ◽  
Vol 37 (5) ◽  
Author(s):  
Honglin Chen ◽  
Liping Liu ◽  
Lixia Wang ◽  
Suhua Wang ◽  
Ming Li Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Germplasm Collection ◽  
Adzuki Bean ◽  
Chinese Germplasm

Application of resistance gene analog markers to analyses of genetic structure and diversity in rice

Genome ◽  
2013 ◽  
Vol 56 (7) ◽  
pp. 377-387 ◽  
Author(s):  
Juansheng Ren ◽  
Yuchao Yu ◽  
Fangyuan Gao ◽  
Lihua Zeng ◽  
Xianjun Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Resistance Gene ◽  
Ssr Markers ◽  
Plant Disease Resistance ◽  
Germplasm Collection ◽  
Resistance Gene Analog ◽  
Disease Resistance Gene ◽  
Plant Disease Resistance Gene ◽  
Genetic Structure And Diversity

Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana.

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